BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6008743.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.result/quality.files/genome_results.txt >>>>>>> Reference number of bases = 3,095,693,983 bp number of contigs = 25 >>>>>>> Globals number of windows = 424 number of reads = 2,316,467 number of mapped reads = 995,948 (42.99%) number of supplementary alignments = 3,497 (0.15%) number of secondary alignments = 0 number of mapped bases = 60,386,684 bp number of sequenced bases = 60,352,130 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 46,503 duplication rate = 3.21% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 40.5293 >>>>>>> ACTG content number of A's = 14,761,971 bp (24.46%) number of C's = 11,392,774 bp (18.88%) number of T's = 18,141,589 bp (30.06%) number of G's = 16,053,133 bp (26.6%) number of N's = 2,663 bp (0%) GC percentage = 45.48% >>>>>>> Mismatches and indels general error rate = 0.0092 number of mismatches = 549,776 number of insertions = 4,837 mapped reads with insertion percentage = 0.48% number of deletions = 21,664 mapped reads with deletion percentage = 2.15% homopolymer indels = 45.42% >>>>>>> Coverage mean coverageData = 0.0195X std coverageData = 0.2067X There is a 1.72% of reference with a coverageData >= 1X There is a 0.14% of reference with a coverageData >= 2X There is a 0.03% of reference with a coverageData >= 3X There is a 0.02% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0.01% of reference with a coverageData >= 6X There is a 0% of reference with a coverageData >= 7X There is a 0% of reference with a coverageData >= 8X There is a 0% of reference with a coverageData >= 9X There is a 0% of reference with a coverageData >= 10X There is a 0% of reference with a coverageData >= 11X There is a 0% of reference with a coverageData >= 12X There is a 0% of reference with a coverageData >= 13X There is a 0% of reference with a coverageData >= 14X There is a 0% of reference with a coverageData >= 15X There is a 0% of reference with a coverageData >= 16X There is a 0% of reference with a coverageData >= 17X There is a 0% of reference with a coverageData >= 18X There is a 0% of reference with a coverageData >= 19X There is a 0% of reference with a coverageData >= 20X There is a 0% of reference with a coverageData >= 21X There is a 0% of reference with a coverageData >= 22X There is a 0% of reference with a coverageData >= 23X There is a 0% of reference with a coverageData >= 24X There is a 0% of reference with a coverageData >= 25X There is a 0% of reference with a coverageData >= 26X There is a 0% of reference with a coverageData >= 27X There is a 0% of reference with a coverageData >= 28X There is a 0% of reference with a coverageData >= 29X There is a 0% of reference with a coverageData >= 30X There is a 0% of reference with a coverageData >= 31X There is a 0% of reference with a coverageData >= 32X There is a 0% of reference with a coverageData >= 33X There is a 0% of reference with a coverageData >= 34X There is a 0% of reference with a coverageData >= 35X There is a 0% of reference with a coverageData >= 36X There is a 0% of reference with a coverageData >= 37X There is a 0% of reference with a coverageData >= 38X There is a 0% of reference with a coverageData >= 39X There is a 0% of reference with a coverageData >= 40X There is a 0% of reference with a coverageData >= 41X There is a 0% of reference with a coverageData >= 42X There is a 0% of reference with a coverageData >= 43X There is a 0% of reference with a coverageData >= 44X There is a 0% of reference with a coverageData >= 45X There is a 0% of reference with a coverageData >= 46X There is a 0% of reference with a coverageData >= 47X There is a 0% of reference with a coverageData >= 48X There is a 0% of reference with a coverageData >= 49X There is a 0% of reference with a coverageData >= 50X There is a 0% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 5458532 0.021899772919723236 0.2585770065616422 chr2 243199373 5161604 0.021223755375389064 0.30767094527506456 chr3 198022430 4161414 0.021014861801261605 0.16781973263983516 chr4 191154276 3084646 0.01613694479949797 0.15206905414787805 chr5 180915260 2913320 0.01610322976624526 0.14588686788664929 chr6 171115067 3167520 0.0185110525655815 0.17218585241078796 chr7 159138663 3565997 0.02240811210032599 0.30256934796877877 chr8 146364022 3963572 0.0270802342395319 0.21574936170201786 chr9 141213431 1960392 0.01388247552741637 0.18290052636348486 chr10 135534747 3330808 0.024575306876840963 0.2253551165592251 chr11 135006516 2693886 0.01995374801020715 0.19841181683791445 chr12 133851895 2746295 0.020517415909576776 0.17133270510585075 chr13 115169878 1571600 0.013645929189922386 0.1423379556763839 chr14 107349540 1961687 0.01827382772203775 0.1566686298437648 chr15 102531392 1807842 0.017632082864923945 0.15996601203340907 chr16 90354753 1712713 0.018955427834549003 0.1732092817638452 chr17 81195210 2000413 0.024637081423891878 0.19780464887300003 chr18 78077248 1213501 0.015542312659380617 0.25338844532168264 chr19 59128983 1568858 0.026532808791925273 0.22866534515162223 chr20 63025520 1426423 0.022632466975282393 0.17655261580119136 chr21 48129895 732517 0.015219584418374484 0.14687097449884476 chr22 51304566 903376 0.017608101391989164 0.16500064426399136 chrMT 16571 29998 1.8102709552833263 1.955041845741363 chrX 155270560 3064413 0.019735956384777643 0.17751748801631007 chrY 59373566 185357 0.0031218775035341483 0.0764471629451394